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The increasing demand for flexibility of automated production systems also affects the automated material flow systems (aMFS) they contain and demands reconfigurable systems. However, the centralized control concept usually applied in aMFS hinders an easy adaptation, as the entire control software has to be re-tested, when manually changing sub-parts of the control. As adaption and subsequent testing are a time-consuming task, concepts for splitting the control from one centralized to multiple, decentralized control nodes are required. Therefore, this paper presents a holistic agent-based control concept for aMFS, whereby the system is divided into so-called automated material flow modules (aMFM), each being controlled by a dedicated module agent. The concept allows the reconfiguration of aMFS, consisting of heterogeneous, stationary aMFM, during runtime. Furthermore, it includes aspects such as uniform agent knowledge bases through metamodel-based development, a communication ontology considering different information types and properties, strategic route optimization in decentralized control architecture and a visualization concept to make decisions of the module agents comprehensible to operators and maintenance staff. The evaluation of the concept is performed by means of material flow simulations as well as a prototypical implementation on a lab-sized demonstrator.